blastall to Cytoscape 3.0 +

Question

[dslade]

Hi everyone,

First, I am no expert in bioinformatics, but I have used command line blast with cytoscape in the past to produce networks. But I was hoping to get some help with a blastall data set (-m 8) in .txt format and how I can turn this into a network in Cytoscape 3.2 or above? I was previously using version 2.7 because Blast2similarity worked on it, but there has to be a better way to cluster my proteins in the new version.

Big fan of the forum and how generous everyone is here. Hoping to contribute in the future, and I thank you in advance.

Cheers

Answer 1

[scooter]

Hi there,

Sure! Basically what you want to do is to take your blastall output and convert that to a simple interaction file (SIF) format that looks something like this:

Gene ss Gene score
Gene ss Gene score
...

where score is the Blast E-value. You can then read that into Cytoscape easily. I would definitely recommend Cytoscape 3.9.1 rather than 3.2 -- 3.9 has a number of enhancements that allow it to work better for larger networks.

Hope this helps!

-- scooter